fix: parse grRules into a tree; fix removeGenes, expandModel, findPotentialErrors - #673
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…lErrors Three functions each reasoned about grRules by searching the raw string, and each got it wrong in a different way. They now share one parse tree. New in utils/: parseGrRule (tokenise + recursive descent), isDnfGrRule, grRuleToDNF, grRuleToString. Operators are matched as whole words, so a gene called RAND1 is a gene, and "10" is never confused with "100". raven-toolbox gets this for free from cobra's Python AST (utils/gpr.py, manipulation/expand.py); MATLAB has no equivalent, so the tree is built here. isDnfGrRule mirrors _is_dnf_node/_contains_or and grRuleToDNF mirrors _node_to_dnf node for node. removeGenes (R2): removeGeneFromRule used an unanchored strfind over the ' or '-split rule, so removing gene "10" from "10 or 100" also matched "100" and left the reaction with no grRule at all while gene 100 stayed in the model -- the association was destroyed, silently, and standardizeGrRules then zeroed the rxnGeneMat row. Numeric Entrez/HGNC ids make this the norm rather than the exception in the tINIT/HPA human workflow, and findGeneDeletions and runSimpleOptKnock mispredict essentiality off the result. Both subfunctions now walk the tree, comparing gene ids with strcmp. This also retires the last eval-based grRule evaluation in the codebase. expandModel (EX1): stripped every parenthesis and split on ' or ', which destroys precedence. "g1 and (g2 or g3)" expanded to "g1 and g2" and "g3" -- the second isozyme silently lost its mandatory g1 subunit, so a g1 knockout was predicted viable when it is lethal. Isozymes are now the DNF clauses. The reaction count comes from the clauses too: "(g1 or g2) and (g3 or g4)" has two or:s but four isozymes, and the old preallocation sized for three. rxnToCheck now lists only rules that genuinely needed distributivity, not every rule containing ' and '. findPotentialErrors (S2): the one-level split flagged valid DNF such as "((G1 and G2) or G3)" and "(G1 or G2) or (G3 and G4)". That was worse than cosmetic: standardizeGrRules skips flagged rules, so a false positive meant the rule was never repaired and kept the brackets the function exists to remove. Unparseable rules are now reported as issues rather than skipped. Also fix a pre-existing crash in expandModel: cpyIndices was a row, and indexing a 1x1 field takes the orientation of the index, so every concatenation failed on a single-reaction model. Tests: nothing under testing/ exercised grRules at all. Adds parser coverage to tUtils and regression tests to tManipulation for each defect above, using the reproductions as the anchors.
Function test results259 tests 237 ✅ 1m 2s ⏱️ Results for commit 14e8e2c. |
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Main improvements in this PR:
parseGrRule,grRuleToDNF,isDnfGrRule,grRuleToString.removeGenesremoved the wrong gene's association when one gene id was a substring of another.expandModeldropped mandatory subunits when expanding rules mixingandandor.findPotentialErrorsflagged valid DNF rules as errors, which also preventedstandardizeGrRulesfrom repairing them.tUtils.mandtManipulation.m.Instructions on merging this PR:
develop3as target branch, and will be resolved with a squash-merge.